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The lack of standardized and automated methodologies poses a challenge for the analysis and interpretation of RNA sequencing data. We critically compare and evaluate state-of-the-art bioinformatics approaches and present a workflow that integrates the best performing data analysis, data evaluation and annotation methods in a\n                      <jats:bold>T<\/jats:bold>\n                      ransparent,\n                      <jats:bold>R<\/jats:bold>\n                      eproducible and\n                      <jats:bold>A<\/jats:bold>\n                      utomated\n                      <jats:bold>P<\/jats:bold>\n                      ipe\n                      <jats:bold>LINE<\/jats:bold>\n                      (TRAPLINE) for RNA sequencing data processing (suitable for Illumina, SOLiD and Solexa).\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Comparative transcriptomics analyses with TRAPLINE result in a set of differentially expressed genes, their corresponding protein-protein interactions, splice variants, promoter activity, predicted miRNA-target interactions and files for single nucleotide polymorphism (SNP) calling. The obtained results are combined into a single file for downstream analysis such as network construction. We demonstrate the value of the proposed pipeline by characterizing the transcriptome of our recently described stem cell derived antibiotic selected cardiac bodies ('aCaBs').<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      TRAPLINE supports NGS-based research by providing a workflow that requires no bioinformatics skills, decreases the processing time of the analysis and works in the cloud. The pipeline is implemented in the biomedical research platform Galaxy and is freely accessible via\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.sbi.uni-rostock.de\/RNAseqTRAPLINE\">www.sbi.uni-rostock.de\/RNAseqTRAPLINE<\/jats:ext-link>\n                      or the specific Galaxy manual page (\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/usegalaxy.org\/u\/mwolfien\/p\/trapline---manual\">https:\/\/usegalaxy.org\/u\/mwolfien\/p\/trapline---manual<\/jats:ext-link>\n                      ).\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-015-0873-9","type":"journal-article","created":{"date-parts":[[2016,1,6]],"date-time":"2016-01-06T06:21:08Z","timestamp":1452061268000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":38,"title":["TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation"],"prefix":"10.1186","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1887-4772","authenticated-orcid":false,"given":"Markus","family":"Wolfien","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian","family":"Rimmbach","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ulf","family":"Schmitz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia Jeannine","family":"Jung","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Krebs","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gustav","family":"Steinhoff","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"David","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olaf","family":"Wolkenhauer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2016,1,6]]},"reference":[{"issue":"7231","key":"873_CR1","doi-asserted-by":"publisher","first-page":"768","DOI":"10.1038\/news.2009.86","volume":"457","author":"EC Hayden","year":"2009","unstructured":"Hayden EC. 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